What are the inputs for Functional Analysis module?

This module accepts either a complete (not just significant!) peak list or a complete peak intensity table.

Peak List (version 1): The Function Analysis module accepts either one of the three formats below:

  • A three column table containing the m/z features, p-values, and statistical scores;
  • A two-column table containing m/z features and either p-values or t-scores;
  • A one-column table ranked by either p-values or t-scores.

All inputted files must be in .txt format. If the input is a three column table, both the mummichog and GSEA algorithms (and their combination) can be applied. If only p-values (or ranked by p-values) are provided, then only the mummichog algorithm will be applied. If only t-scores (or ranked by t-scores) are provided, then only the GSEA algorithm will be applied.

Peak List (version 2): With Version 2 of mummichog in Functional Analysis module, retention time can be included as a new column with the “rt” or “r.t” heading. The maximum number of columns that can be uploaded is 5: “m.z”, “r.t”, “p.value”, “t.score” and “mode”.

Peak Intensity Table: This table should contain sample class labels and feature IDs with mass and/or retention times. See examples below:

If I want to upload a peak-list, do I need to use raw p-values or q-values (corrected for multiple hypotheses testing)?

For these algorithms (mummichog and GSEA), p-values are only used to rank peaks and are not applied as a cut-off, so multiple hypothesis correction is not a concern. Sometimes multiple hypothesis correction results in many distinct p-values being replaced by the same value (ie. all ‘rounded up’ to 1), erasing the ranking. For this reason, using raw p-values is better.